rs201868215

Variant names:

• chr8-1565865-C-G
• NM_001346810.2:c.1413C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-1565865-C-G
• chr8-1565865-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001346810.2(DLGAP2):​c.1413C>G​(p.Ile471Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: DLGAP2 NM_001346810.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

Genes affected

DLGAP2 (HGNC:2906): (DLG associated protein 2) The product of this gene is a membrane-associated protein that may play a role in synapse organization and signalling in neuronal cells. This gene is biallelically expressed in the brain, however, only the paternal allele is expressed in the testis (PMID:18055845). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2014]

DLGAP2-AS1 (HGNC:50467): (DLGAP2 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08722502).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLGAP2	NM_001346810.2	c.1413C>G	p.Ile471Met	missense_variant	Exon 6 of 15	ENST00000637795.2	NP_001333739.1
DLGAP2-AS1	NR_103863.1	n.358-127G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLGAP2	ENST00000637795.2	c.1413C>G	p.Ile471Met	missense_variant	Exon 6 of 15	5	NM_001346810.2	ENSP00000489774.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1458448 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 725200

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000253

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.032
DANN	Benign	0.97
DEOGEN2	Benign	0.016	T;T;T
Eigen	Benign	-0.92
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.20	N
LIST_S2	Benign	0.75	T;T;T
M_CAP	Benign	0.0060	T
MetaRNN	Benign	0.087	T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-0.40	.;N;.
PrimateAI	Benign	0.46	T
REVEL	Benign	0.087
Sift4G	Uncertain	0.028	.;.;D
Polyphen		0.57	.;P;.
Vest4		0.17
MutPred		0.13		.;Loss of catalytic residue at I470 (P = 0.0326);.;
MVP		0.17
MPC		0.10
ClinPred		0.42	T
GERP RS		-9.1
Varity_R		0.037
gMVP		0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-1514031;